Contacts of the helix formed by residues 12 - 40 (chain D) in PDB entry 2YW7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 12 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASP* 1.3 82.4 - - - +
13D LYS* 1.3 67.1 + - - +
14D ALA* 3.0 5.4 + - - +
15D SER* 3.1 23.1 + - - +
16D ASP* 3.4 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG* 6.4 1.6 - - - +
125B GLU* 5.2 11.5 + - - +
11D ASP 4.4 3.3 - - - +
12D LYS* 1.3 80.0 - - - +
14D ALA* 1.3 58.4 + - - +
16D ASP* 4.2 2.7 + - - +
17D VAL* 3.3 29.2 + - + +
130D LEU* 3.7 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASP 5.5 2.4 - - - +
12D LYS 3.0 2.8 - - - +
13D LYS* 1.3 76.0 - - - +
15D SER* 1.3 57.7 + - - +
16D ASP 3.0 2.2 - - - -
17D VAL* 2.7 14.9 + - - -
18D ALA* 2.6 35.3 + - + +
75D LEU* 4.1 37.5 - - + +
77D LYS* 6.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASP 5.1 2.9 - - - -
12D LYS* 3.1 24.8 + - - +
14D ALA* 1.3 77.5 - - - +
16D ASP* 1.3 63.2 + - - +
19D ASP* 3.6 19.9 + - - +
77D LYS* 4.3 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LYS* 3.4 35.8 + - - +
13D LYS* 4.5 3.4 - - - +
14D ALA 2.8 4.0 + - - -
15D SER* 1.3 75.0 - - - +
17D VAL* 1.3 66.1 + - + +
19D ASP* 3.5 5.4 + - - +
20D LEU* 3.0 21.1 + - - +
130D LEU* 5.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LYS* 3.3 21.0 + - + +
14D ALA* 2.7 9.4 + - - +
16D ASP* 1.3 72.7 - - - +
18D ALA* 1.3 60.0 + - - +
20D LEU* 2.9 25.6 + - - +
21D LEU* 2.9 16.7 + - + +
75D LEU* 3.7 23.3 - - + -
127D LEU* 3.8 19.5 - - + -
130D LEU* 3.5 34.3 - - + +
131D ASP* 3.9 20.4 - - + +
134D SER* 4.2 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ALA* 2.6 22.5 + - + +
15D SER 4.7 0.2 - - - +
17D VAL* 1.3 75.5 - - - +
19D ASP* 1.3 57.1 + - - +
21D LEU* 2.9 24.6 + - - +
22D GLN* 2.9 14.9 + - - +
72D ILE* 3.8 13.7 - - + +
75D LEU* 4.5 18.8 - - + -
77D LYS* 4.3 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D SER 3.6 18.1 + - - +
16D ASP* 3.5 5.6 + - - +
17D VAL 3.3 0.4 - - - -
18D ALA* 1.3 77.7 - - - +
20D LEU* 1.3 62.4 + - - +
22D GLN* 3.1 25.7 + - - +
23D LYS* 3.2 16.9 + - - +
77D LYS* 5.4 9.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASP 3.0 14.1 + - - +
17D VAL* 2.9 16.6 + - - +
19D ASP* 1.3 77.1 - - - +
21D LEU* 1.3 59.1 + - + +
23D LYS* 4.0 13.3 + - - +
24D GLN* 3.7 15.2 + - - +
123D SER* 3.4 48.7 + - - +
126D LYS* 3.9 33.7 - - + +
127D LEU* 4.0 21.5 - - + -
130D LEU* 6.2 2.2 - - + -
138D LEU* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D VAL* 2.9 13.5 + - + +
18D ALA* 2.9 8.5 + - - +
20D LEU* 1.3 78.5 - - + +
22D GLN* 1.3 53.3 + - - +
23D LYS 3.4 0.2 - - - -
24D GLN* 3.1 5.7 - - + +
25D LEU* 2.7 30.5 + - - +
68D VAL* 3.3 22.9 - - + +
71D ARG* 3.6 26.5 - - + -
72D ILE* 3.5 15.9 - - + -
75D LEU* 3.9 13.7 - - + -
127D LEU* 4.8 3.6 - - + -
134D SER* 3.6 43.1 - - - +
137D LEU* 5.1 3.4 - - + -
138D LEU* 4.5 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ALA 2.9 12.0 + - - +
19D ASP* 3.1 21.9 + - - +
21D LEU* 1.3 74.9 - - - +
23D LYS* 1.3 65.2 + - + +
25D LEU* 3.3 9.3 + - - +
26D SER* 3.0 39.1 + - - -
72D ILE* 3.5 12.8 - - + +
78D SER 4.5 2.8 - - - +
79D PRO* 4.0 5.0 - - - +
80D LYS* 3.1 49.2 + - + +
85D ALA* 3.4 11.5 - - - +
89D ASP* 3.1 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ASP* 3.2 10.9 + - - +
20D LEU* 4.1 18.4 - - + +
21D LEU 3.4 0.2 - - - -
22D GLN* 1.3 77.5 - - + +
24D GLN* 1.3 57.6 + - - +
26D SER* 3.4 2.4 + - - -
27D THR* 3.0 32.9 + - - +
89D ASP* 3.3 44.5 - - + +
91D THR* 3.7 22.1 - - + +
92D TRP* 5.6 0.2 - - - -
119D ASP* 4.3 16.2 + - - -
123D SER* 5.8 2.9 - - - +
126D LYS* 5.6 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU 3.7 8.1 + - - +
21D LEU* 3.1 17.2 + - + +
23D LYS* 1.3 77.2 - - - +
25D LEU* 1.3 65.7 + - - +
27D THR* 3.1 23.0 + - - +
28D TYR* 2.9 47.8 + - + +
68D VAL* 4.3 3.8 - - + -
119D ASP* 4.9 4.0 - - - +
120D THR* 2.7 47.4 + - - +
123D SER* 4.5 8.0 + - - +
138D LEU* 3.5 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU 2.7 17.0 + - - +
22D GLN* 3.4 18.4 - - - +
24D GLN* 1.3 73.1 - - - +
26D SER* 1.3 58.4 + - - +
28D TYR* 3.1 7.1 + - - +
29D ASN* 3.0 50.2 + - - +
65D ALA* 3.1 34.5 - - + +
68D VAL* 3.7 15.0 - - + +
69D ALA* 4.1 14.4 - - + -
72D ILE* 4.0 8.5 - - + -
79D PRO* 5.0 1.1 - - + -
80D LYS 3.5 28.9 - - - +
81D GLY* 4.0 1.8 - - - +
40I TRP* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D GLN* 3.0 19.3 + - - -
23D LYS 3.9 2.5 - - - -
25D LEU* 1.3 71.9 - - - +
27D THR* 1.3 66.8 + - - +
28D TYR 3.0 1.6 - - - -
29D ASN* 3.9 1.9 - - - +
30D ASP* 2.9 27.4 + - - +
80D LYS 4.0 2.6 + - - -
86D ILE* 3.4 40.3 + - - +
89D ASP* 2.9 30.1 + - - -
90D ARG* 5.5 3.4 - - - -
92D TRP* 5.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LYS* 3.0 17.7 + - - +
24D GLN* 3.1 21.3 + - - +
26D SER* 1.3 75.9 - - - +
28D TYR* 1.3 60.3 + - + +
30D ASP* 3.7 2.6 - - - +
31D LEU* 3.1 24.4 + - - +
89D ASP 5.7 0.3 + - - -
92D TRP* 3.3 33.9 - - + -
116D VAL* 3.5 42.7 - - + +
119D ASP* 4.8 8.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLN* 2.9 50.8 + - + +
25D LEU 3.1 4.7 + - - +
26D SER 3.0 0.6 - - - -
27D THR* 1.3 79.0 - - + +
29D ASN* 1.3 56.6 + - - +
30D ASP 3.0 1.6 - - - -
31D LEU* 2.7 28.2 + - + +
32D HIS* 2.7 18.0 + - - -
61D VAL* 3.6 25.7 - - + +
64D TYR* 3.8 21.3 - + + -
65D ALA* 3.9 16.4 - - + -
68D VAL* 4.0 13.7 - - + -
116D VAL* 4.7 10.1 - - + -
120D THR* 4.6 0.6 + - - -
141D HIS* 2.8 44.2 + + - +
145D LEU* 4.3 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU* 3.0 45.8 + - - +
26D SER 3.9 1.1 - - - +
28D TYR* 1.3 75.1 - - - +
30D ASP* 1.3 63.3 + - - +
32D HIS* 3.6 24.6 + - - +
33D LEU* 3.3 26.2 + - - +
65D ALA* 3.7 14.4 - - - +
81D GLY* 3.5 22.2 - - - -
86D ILE* 3.6 23.1 - - + +
33I LEU* 4.6 9.4 - - + +
40I TRP* 3.9 10.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D SER 2.9 17.8 + - - +
27D THR 3.7 4.2 - - - +
29D ASN* 1.3 76.2 - - - +
31D LEU* 1.3 67.9 + - - +
33D LEU* 3.0 7.4 + - - +
34D THR* 3.0 38.4 + - - -
86D ILE* 4.5 10.3 - - + +
90D ARG* 4.5 1.6 + - - -
92D TRP* 3.1 37.8 + - + -
94D ASP* 4.4 6.3 - - - +
112D VAL* 5.8 3.1 - - - +
83I PRO* 3.5 31.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D THR 3.1 14.1 + - - +
28D TYR* 2.7 15.9 + - + +
30D ASP* 1.3 79.4 + - - +
32D HIS* 1.3 56.8 + - - +
34D THR* 3.3 5.0 + - - -
35D LEU* 2.7 45.4 + - + +
61D VAL* 4.1 17.7 - - + -
109D LEU* 5.9 1.6 - - + -
112D VAL* 4.7 9.2 - - + -
113D TYR* 3.5 40.2 - - + +
116D VAL* 3.9 37.2 - - + -
145D LEU* 4.4 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D TYR 2.7 14.5 + - - -
29D ASN* 3.6 43.8 + - - -
31D LEU* 1.3 74.9 - - - +
33D LEU* 1.3 77.7 + - + +
35D LEU* 4.0 6.3 - - - -
36D LYS* 3.1 25.5 + - - +
58D VAL* 3.4 23.9 - - + +
61D VAL* 3.6 17.5 - - + -
62D ARG* 3.8 30.7 - - + +
65D ALA* 4.6 2.8 - - + +
32I HIS* 4.8 5.2 - + - -
33I LEU* 4.2 13.0 - - + +
62I ARG* 5.8 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ASN 3.3 16.4 - - - +
30D ASP 3.0 7.2 + - - +
32D HIS* 1.3 97.7 + - + +
34D THR* 1.3 56.1 + - - +
35D LEU 3.2 0.2 - - - -
36D LYS* 3.2 10.3 + - + +
37D HIS* 2.5 35.2 + - - +
40D TRP* 5.4 1.5 - - + -
86D ILE* 4.4 10.3 - - + -
29I ASN* 4.4 10.5 - - + +
32I HIS* 3.8 22.2 - - + +
33I LEU* 3.5 30.1 - - + -
81I GLY 3.4 21.6 - - - +
83I PRO* 4.8 9.4 - - + -
86I ILE* 4.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ASP* 3.0 29.2 + - - -
31D LEU* 3.4 11.4 - - + -
33D LEU* 1.3 71.8 - - - +
35D LEU* 1.3 56.7 + - - +
37D HIS* 3.0 9.3 + - - +
38D VAL* 2.7 33.3 + - - +
95D TYR* 3.5 48.0 + - + +
109D LEU* 4.4 11.0 - - + -
112D VAL* 4.6 10.1 - - + -
81I GLY 4.4 0.8 + - - -
82I THR* 5.2 3.5 - - - +
83I PRO* 4.8 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU* 2.7 40.3 + - + +
32D HIS* 3.6 7.0 - - - +
34D THR* 1.3 71.8 - - - +
36D LYS* 1.3 57.1 + - - +
38D VAL* 3.1 7.3 + - - +
39D HIS* 2.9 26.9 + - - +
54D ILE* 3.6 31.9 - - + +
57D GLN* 3.4 29.2 - - + +
58D VAL* 3.7 21.5 - - + +
61D VAL* 4.4 3.1 - - + -
109D LEU* 3.8 32.3 - - + -
113D TYR* 4.7 0.7 - - + +
148D PHE* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D HIS 3.1 13.5 + - - +
33D LEU* 3.3 12.6 - - + +
35D LEU* 1.3 79.6 - - - +
37D HIS* 1.3 61.7 + - - +
39D HIS* 3.2 15.4 + - + +
40D TRP* 3.2 52.1 + - + +
55D ASP* 4.6 13.1 + - - +
58D VAL* 4.4 23.6 - - + +
62I ARG* 5.3 10.3 - - - +
66I ASP* 3.3 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU 2.5 18.9 + - - +
34D THR* 3.1 12.6 - - - +
36D LYS* 1.3 69.8 - - - +
38D VAL* 1.3 65.5 + - - +
40D TRP* 2.9 15.3 + - - -
41D ASN* 2.7 37.6 + - + +
95D TYR* 3.4 32.1 + + - -
97D VAL 2.9 21.0 + - - -
98D GLU* 5.1 2.7 - - + +
78I SER* 6.0 0.7 - - - -
79I PRO 3.0 29.5 + - - -
80I LYS* 4.1 6.7 - - + -
81I GLY 3.4 20.5 + - - +
82I THR* 4.1 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D THR 2.7 20.0 + - - +
35D LEU* 3.5 7.2 - - - +
37D HIS* 1.3 70.8 - - - +
39D HIS* 1.3 54.6 + - - +
41D ASN 2.7 21.7 + - - -
42D VAL* 2.8 31.5 + - + +
50D VAL* 4.6 1.1 - - + -
54D ILE* 3.5 17.5 - - + -
95D TYR* 3.3 37.7 - - + +
105D HIS* 3.2 28.3 - - + +
106D LEU* 5.5 2.0 - - + +
109D LEU* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D LEU 2.9 12.4 + - - +
36D LYS* 3.3 22.6 - - + +
37D HIS 3.1 0.4 - - - -
38D VAL* 1.3 76.9 - - - +
40D TRP* 1.3 66.8 + - + +
41D ASN 3.3 0.7 + - - -
42D VAL* 4.4 5.3 + - - +
51D HIS* 3.3 61.8 + + - -
54D ILE* 4.0 18.8 - - + +
55D ASP* 2.8 40.8 + - - -
66I ASP* 5.7 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 6.3 1.3 - - + -
36D LYS* 3.2 39.7 + - + +
37D HIS* 2.9 14.0 + - - +
39D HIS* 1.3 87.6 + - - +
41D ASN* 1.3 69.7 + - - +
42D VAL 3.9 1.6 - - - -
99D ARG* 5.2 2.6 - - - +
25I LEU* 4.0 15.3 - - + -
29I ASN* 4.3 13.0 - - - -
65I ALA* 3.3 23.6 - - + -
66I ASP* 3.7 29.8 + - - +
69I ALA* 3.8 23.0 - - + +
70I GLU* 5.6 3.4 - - + -
73I ALA* 4.7 8.9 - - + +
79I PRO* 4.0 32.3 - - + +
81I GLY* 4.0 24.0 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il